4D-BioReconX

a bioinformatic framework for reconstructing 4D spatial transcriptomics atlas and spatiotemporal analyses+

4D-BioReconX is a scalable and versatile framework designed to construct a comprehensive four-dimensional (4D) spatial transcriptomics atlas of whole animals at single-cell resolution. This approach enables us to track the intricate spatiotemporal dependencies of morphogenetic gradients and regenerative patterning. It runs based on spatial transcriptomics data, such as Stereo-seq (spatial enhanced resolution omics sequencing) data. Notably, we are still working on the improvement of performance and calculation efficiency.

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Highlights

• To our knowledge, this represents the first framework for achieving single-cell resolved, four-dimensional (4D) transcriptional and anatomical reconstruction of adult animals at the molecular level. Leveraging Stereo-seq, we meticulously profiled

• Our analysis models the spatiotemporal reprogramming of positional information during regeneration. We unveil genes responding to regeneration with

• We identified a Regeneration-Organizing Domain (ROD) and the underlying regulatory mechanisms. While organizers in development are known to establish

Workflow